Merge branch 'gn2'

2 files changed, 42 insertions, 0 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 0c4436c..75b9de7 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -44,6 +44,7 @@
   #:use-module (gnu packages zip)
   #:use-module (gnu packages bootstrap)
   #:use-module (gn packages python)
+  #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
 (define-public my-deploy
@@ -379,6 +380,7 @@ association studies (GWAS).")
               ("redis" ,redis)
               ("mysql" ,mysql)
               ("gemma" ,gemma-git)
+              ("pylmm-gn2" ,pylmm-gn2)
               ("plink2" ,plink-ng)
               ("nginx" ,nginx)
               ("python2-flask" ,python2-flask)
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 065826e..2d83816 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -148,3 +148,43 @@
      "R/lmmlite")
     (home-page "https://github.com/kbroman/")
     (license license:asl2.0)))
+
+(define-public pylmm-gn2
+  (let ((commit "3c6d1cac8"))
+  (package
+    (name "pylmm-gn2")
+    (version (string-append "1.0-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/genenetwork/pylmm.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964"))))
+    (build-system python-build-system)
+    (inputs `(
+              ("python2-setuptools" ,python2-setuptools)
+              ("python2-scipy" ,python2-scipy)
+              ("python2-numpy" ,python2-numpy)
+              ))
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f        ; no 'setup.py test'
+       #:phases
+       (modify-phases %standard-phases
+         (add-before
+          'build 'change-paths
+          (lambda* (#:key outputs #:allow-other-keys)
+                   (let ((out (assoc-ref outputs "out")))
+                     (substitute* "scripts/pylmm_redis"
+                                  (("/usr/bin/python") (which "python"))
+                                  (("\\$PACKAGEDIR") (string-append out "/lib/python2.7/site-packages")))
+                     ))))))
+
+    (home-page "http://genenetwork.org/")
+    (synopsis "LMM resolver")
+    (description "Fast and lightweight linear mixed-model (LMM) solver
+for use in genome-wide association studies (GWAS).")
+    (license license:agpl3+))))